MVAM (Prometheus Refit)-> Arguably useful, what you'll hear depends on the player using it.
Saucer Separation (Galaxy Refit)-> Almost useless, except for the turn rate buff you get from being separated, though you lose quite a bit of healing ability. Kind of a hassle if you're saucer gets blown up.
Transwarp (Excelsior Retrofit) -> It's ok, not a must have feature, but it comes in handy from time to time. It's more of a nice thing to have.
Ablative Armor (Intrepid Refit) -> Useful in PvP as for tanking or making a break for it. Intrepids make some of the best tanks.
Cloaking Device (Defiant Refit, Galaxy-X) -> As useful as the Klingon's cloak, but slightly more effective only because FvF and Klingon players rarely expect it.
Phaser Lance (Galaxy-X) -> Needs practice to use effectively, most players I've seen aren't very good with it, but with some work it can be deadly. Also, misses a lot.
Tachyon Detection Grid (Nebula Refit) -> It's a situation ability. Incredibly useful when fighting Klingons who like to Cloak, practically worthless in any other area, besides lagging out players with low end graphics cards.
Launch Support Craft (D'kyr) -> You could argue that it's useful, but experience shows us that it doesn't really make a difference.
Honestly, the big appeal of the Refit ships is the BOff layouts, not the inherent abilities.
I dunno, I think the Excelsior-R has a pretty balanced setup. It sacrifices some survivability for that Lt. Cmdr Tac Slot and superior maneauverability. I'm not a fan of the ship, myself but It's seems pretty well in line.